Finding overlap between two same frames tracked by different tracker with refrence to ground truth where i have date is [ X Y height and width ] of the respective bounding boxes.

hi i have to find overlap between two frames with bounding boxes where one is ground truth and other is tracked by trackers. the data i have available is x, y, width, and height of the centroid of bounding boxes but there are multiple objects in the frame so i need to subtract everything from frame except my object and find overlapping pixels. any help regarding this will be a great breakthrough for my project. thanks

   clear all;
    close all;

    filename = 'Test_Seq.avi';

    mmReaderObj = mmreader(filename);
    %[vidFrames mmReaderObj] = LoadVideoFile(filename);
    numFrames = mmReaderObj.NumberOfFrames;
    GroundTruth = ones(numFrames, 5);
    GroundTruth(:,1) = 1:numFrames;
    %GroundTruth(:,8) = 0;

    n = 2;
    for i = 1:numFrames
    %for i = 1:1
        figure(1);
        imshow(read(mmReaderObj,i));
        [cols rows] = ginput(n);
        width = abs(cols(2)-cols(1));
        height = abs(rows(2)-rows(1));
        x = min(cols)+round(width/2);
        y = min(rows)+round(height/2);
        GroundTruth(i,2:5) = [x y width height];
        frame = i
    end
    GroundTruth = round(GroundTruth);
    WriteMat2TxtFile ('GT2.txt', GroundTruth);

this is the script i use to generate ground truth.